In 2018–2019, Central Europe experienced an unprecedented multi-year drought with severe impacts on society and ecosystems. In this study, we analyzed the impact of this drought on water quality by comparing long-term (1997-2017) nitrate export with 2018–2019 export in a heterogeneous mesoscale catchment. We combined data-driven analysis with process-based modelling to analyze nitrogen retention and the underlying mechanisms in the soils and during subsurface transport. We found a drought-induced shift in concentration-discharge relationships, reflecting exceptionally low riverine nitrate concentrations during dry periods and exceptionally high concentrations during subsequent wet periods. Nitrate loads were up to 70% higher compared to the long-term load-discharge relationship. Model simulations confirmed that this increase was driven by decreased denitrification and plant uptake and subsequent flushing of accumulated nitrogen during rewetting. Fast transit times (<2 months) during wet periods in the upstream sub-catchments enabled a fast water quality response to drought. In contrast, longer transit times downstream (>20 years) inhibited a fast response but potentially contribute to a long-term drought legacy. Overall, our study reveals that severe multi-year droughts, which are predicted to become more frequent across Europe, can reduce the nitrogen retention capacity of catchments, thereby intensifying nitrate pollution and threatening water quality.